import jalview.api.AlignViewportI;
import jalview.api.FeatureColourI;
-import jalview.datamodel.Range;
+import jalview.datamodel.ContiguousI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
+import jalview.util.Platform;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
import java.awt.AlphaComposite;
import java.awt.FontMetrics;
import java.awt.Graphics;
import java.awt.Graphics2D;
+import java.util.ArrayList;
import java.util.List;
public class FeatureRenderer extends FeatureRendererModel
int pady = (y1 + charHeight) - charHeight / 5;
FontMetrics fm = g.getFontMetrics();
+ char s = '\0';
for (int i = featureStart; i <= featureEnd; i++)
{
- char s = seq.getCharAt(i);
- if (Comparison.isGap(s))
+ // colourOnly is just for Overview -- no need to check this again
+
+ if (!colourOnly && Comparison.isGap(s = seq.getCharAt(i)))
{
continue;
}
g.fillRect((i - start) * charWidth, y1, charWidth, charHeight);
- if (colourOnly || !validCharWidth)
+ if (colourOnly)
+ {
+ return true;
+ }
+
+ if (!validCharWidth)
{
continue;
}
}
/**
+ *
+ * BH - this method is never called?
+ *
* Renders the sequence using the given SCORE feature colour between the given
* start and end columns. Returns true if at least one column is drawn, else
* false (the feature range does not overlap the start and end positions).
@Override
public Color findFeatureColour(SequenceI seq, int column, Graphics g)
{
- if (!av.isShowSequenceFeatures())
- {
- return null;
- }
+ // BH 2019.08.01
+ // this is already checked in FeatureColorFinder
+ // if (!av.isShowSequenceFeatures())
+ // {
+ // return null;
+ // }
// column is 'base 1' but getCharAt is an array index (ie from 0)
if (Comparison.isGap(seq.getCharAt(column - 1)))
* applies), or null if no feature is drawn in the range given.
*
* @param g
- * the graphics context to draw on (may be null if colourOnly==true)
+ * the graphics context to draw on (may be null only if t == 1 from
+ * colourOnly==true)
* @param seq
* @param start
* start column
final SequenceI seq, int start, int end, int y1,
boolean colourOnly)
{
+ // from SeqCanvas and OverviewRender
/*
* if columns are all gapped, or sequence has no features, nothing to do
*/
- Range visiblePositions = seq.findPositions(start+1, end+1);
- if (visiblePositions == null || !seq.getFeatures().hasFeatures())
+ ContiguousI visiblePositions;
+ if (!seq.getFeatures().hasFeatures() || (visiblePositions = seq
+ .findPositions(start + 1, end + 1)) == null)
{
return null;
}
+ int vp0 = visiblePositions.getBegin();
+ int vp1 = visiblePositions.getEnd();
+
updateFeatures();
- if (transparency != 1f && g != null)
+ if (transparency != 1f) // g cannot be null here if trans == 1f - BH // && g
+ // != null)
{
- Graphics2D g2 = (Graphics2D) g;
- g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
+ ((Graphics2D) g).setComposite(
+ AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
transparency));
}
/*
* iterate over features in ordering of their rendering (last is on top)
*/
- for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
+ for (int renderIndex = 0, n = renderOrder.length; renderIndex < n; renderIndex++)
{
String type = renderOrder[renderIndex];
- if (!showFeatureOfType(type))
+ if (!seq.hasFeatures(type) || !showFeatureOfType(type))
{
continue;
}
FeatureColourI fc = getFeatureStyle(type);
- List<SequenceFeature> overlaps = seq.getFeatures().findFeatures(
- visiblePositions.getBegin(), visiblePositions.getEnd(), type);
+ List<SequenceFeature> overlaps = seq.getFeatures().findFeatures(vp0,
+ vp1, type);
- filterFeaturesForDisplay(overlaps, fc);
+ // colourOnly (i.e. Overview) can only be here if translucent, so
+ // there is no need to check for filtering
+ if (!colourOnly && fc.isSimpleColour())
+ {
+ filterFeaturesForDisplay(overlaps);
+ }
- for (SequenceFeature sf : overlaps)
+ for (int i = overlaps.size(); --i >= 0;)
{
- Color featureColour = fc.getColor(sf);
+ SequenceFeature sf = overlaps.get(i);
+ Color featureColour = getColor(sf, fc);
if (featureColour == null)
{
- // score feature outwith threshold for colouring
+ /*
+ * feature excluded by visibility settings, filters, or colour threshold
+ */
continue;
}
* restrict to visible positions (or if a contact feature,
* to a single position)
*/
- int visibleStart = sf.getBegin();
- if (visibleStart < visiblePositions.getBegin())
+ int sf0 = sf.getBegin();
+ int sf1 = sf.getEnd();
+ int visibleStart = sf0;
+ if (visibleStart < vp0)
{
- visibleStart = sf.isContactFeature() ? sf.getEnd()
- : visiblePositions.getBegin();
+ visibleStart = sf.isContactFeature() ? sf1 : vp0;
}
- int visibleEnd = sf.getEnd();
- if (visibleEnd > visiblePositions.getEnd())
+ int visibleEnd = sf1;
+ if (visibleEnd > vp1)
{
- visibleEnd = sf.isContactFeature() ? sf.getBegin()
- : visiblePositions.getEnd();
+ visibleEnd = sf.isContactFeature() ? sf0 : vp1;
}
int featureStartCol = seq.findIndex(visibleStart);
- int featureEndCol = sf.begin == sf.end ? featureStartCol : seq
- .findIndex(visibleEnd);
+ int featureEndCol = (sf.begin == sf.end ? featureStartCol
+ : seq.findIndex(visibleEnd));
// Color featureColour = getColour(sequenceFeature);
else
{
*/
- boolean drawn = renderFeature(g, seq,
- featureStartCol - 1,
- featureEndCol - 1, featureColour,
- start, end, y1, colourOnly);
- if (drawn)
- {
- drawnColour = featureColour;
- }
+ boolean drawn = renderFeature(g, seq, featureStartCol - 1,
+ featureEndCol - 1, featureColour, start, end, y1,
+ colourOnly);
+ if (drawn)
+ {
+ drawnColour = featureColour;
+ }
/*}*/
}
}
}
- if (transparency != 1.0f && g != null)
+ if (transparency != 1.0f)
{
/*
* reset transparency
*/
- Graphics2D g2 = (Graphics2D) g;
- g2.setComposite(NO_TRANSPARENCY);
+ ((Graphics2D) g).setComposite(NO_TRANSPARENCY);
}
return drawnColour;
findAllFeatures();
}
+ private List<SequenceFeature> overlaps = (Platform.isJS()
+ ? new ArrayList<>()
+ : null);
+
/**
* Returns the sequence feature colour rendered at the given column position,
* or null if none found. The feature of highest render order (i.e. on top) is
* colour for features enclosing a gapped column. Check for gap before calling
* if different behaviour is wanted.
*
+ * BH 2019.07.30
+ *
+ * Adds a result ArrayList to parameters in order to avoid an unnecessary
+ * construction of that for every pixel checked.
+ *
+ *
* @param seq
* @param column
* (1..)
* @return
*/
- Color findFeatureColour(SequenceI seq, int column)
+ private Color findFeatureColour(SequenceI seq, int column)
{
/*
* check for new feature added while processing
* inspect features in reverse renderOrder (the last in the array is
* displayed on top) until we find one that is rendered at the position
*/
- for (int renderIndex = renderOrder.length
- - 1; renderIndex >= 0; renderIndex--)
+ for (int renderIndex = renderOrder.length; --renderIndex >= 0;)
{
String type = renderOrder[renderIndex];
- if (!showFeatureOfType(type))
+ if (!seq.hasFeatures(type) || !showFeatureOfType(type))
{
continue;
}
- List<SequenceFeature> overlaps = seq.findFeatures(column, column,
- type);
- for (SequenceFeature sequenceFeature : overlaps)
+ if (overlaps != null)
{
- if (!featureGroupNotShown(sequenceFeature))
+ overlaps.clear();
+ }
+ List<SequenceFeature> list = seq.findFeatures(column, type, overlaps);
+ if (list.size() > 0)
+ {
+ for (int i = 0, n = list.size(); i < n; i++)
{
- Color col = getColour(sequenceFeature);
+ SequenceFeature sf = list.get(i);
+ if (featureGroupNotShown(sf))
+ {
+ continue;
+ }
+ Color col = getColour(sf);
if (col != null)
{
return col;
git://source.jalview.org / jalview.git / blobdiff